mapping-bioimage-software: data and code for Mapping bioimage-analysis software adoption in microscopy

Data and code for Mapping bioimage-analysis software adoption in microscopy. The registry contains 30 packages: 22 analysis packages, six microscope-control programs, and MATLAB and Jupyter notebooks as references outside all aggregates. The deep-learning series uses 13 core analysis packages. Jupyter notebooks retain their aliases, notebook category and core scope. Frozen validation designs and labels retain the original 14-package calibration sample. The archive holds processed counts, annotator-labelled validation sets, identifier-only sampling frames, configuration, code and provenance. Data sources: Europe PMC (search API and open-access full text; metadata derived from MEDLINE/PubMed carries the NLM notice that the data may not be current and that NLM does not endorse this work; full text was mined and never redistributed), OpenAlex (CC0), the GitHub REST API (public repository counts), pypistats.org (30-day PyPI download totals from the Python Software Foundation's PyPI BigQuery dataset, CC BY 4.0), the image.sc forum (topic counts only, no posts), Crossref and ORCID (bibliographic metadata, CC0), and MeSH headings from MEDLINE records (2026 MeSH vocabulary, retrieved 15 October 2026). The archive contains no article titles, abstracts or full text. Article text can be rebuilt from identifiers with release/refetch_identifiers.py through Europe PMC. The data are licensed under CC BY 4.0 (LICENSE-DATA) and the code under MIT (LICENSE); this record carries CC BY 4.0 for the data and states the MIT licence for the code. Funding named without a grant identifier: EMBO Installation Grant EMBO-2020-IG-4734; Chan Zuckerberg Initiative Imaging Scientist award (2020-225445); la Caixa Foundation CaixaResearch Health 2025 award (VirusAwareScopes, HR25-00453); Sigrid Juselius Foundation; Cancer Society of Finland; Solutions for Health strategic funding to Åbo Akademi University; Finnish Cancer Institute (K. Albin Johansson Professorship); the Kavli Foundation co-funds the EOSS Cycle 6 award. MEDLINE/PubMed and MeSH data: Courtesy of the U.S. National Library of Medicine; NLM data may not be current, and NLM does not endorse this work.